How do I bevel this object if subdivision surface modiefier is already applied?
Sometimes, it can suit to let the subdivision do the bevel for you.. the resulting curve is not quite the same shape as one you would have made yourself, and can be subtly altered by holding loops a fair way back from the 'bevelled' edge. 

If you don't put the holding loops in, though, the edges between  the bevels are slightly curved, and the large face is not as flat.



The bottom surface is the top topology with three levels of subdivision.